Just do a find-and-replace on every letter in the alphabet, one letter at a time. Open the find-and-replace interface on your scriptwriting program and tell it to replace every "b" in your story with an "a," and every "c" with an "a," then every "d" with an "a." And so on.
Make a copy of your beautiful piece of work before scrambling. This will save tears and heartache for years to come.
Final Draft: file > save as > edit > find
Celtx: edit > replace
Zhura: export > save with layout > save to disk > open file in notepad or similar program notepad > edit replace
*(If you have Word, use it! It is a great tool to user here because you can use wildcards. See below.)
Scripped: coming soon
Plotbot: coming soon
Microsoft Word: In Word you can get fancy and use wildcards. This will allow you to run the find and replace once for the entire document.
Open the file and make a new copy of your novel using "Save As..."
Open the "Find and Replace" dialog box (Edit -> Replace)
Click the "More" button to expand the box
Check the "Use Wildcards" checkbox
In the "Find What" field, put this: [a-zA-Z0-9] (include the square brackets, no spaces before or after)
In the "Replace With" field, put this: a
Click "Replace All"
Save the scrambled file as a text file, and upload away!
The procedure for Open Office is essentially the same, except that Open Office refers to "Regular Expressions" instead of "Wildcards". (Thanks to Peter Dudley for this advice!)